|
| Status |
Public on May 01, 2019 |
| Title |
mouse_colon_mucosal_layer-WT_MCCf_control-rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Colon Mucosal Cells_WT Mcc_control
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype/variation: controls Mccf/f
gender: male
age: 6 wks
diet: control for 10 wks
tissue: normal colon mucosa
cell type: Colon Mucosal Cells
|
| Treatment protocol |
Six-week old mice were given a diet containing 320 ppm sulindac or control feed for 10 weeks. Mice were culled and the mucosal layer was harvested and snap-frozen for RNA extraction. For the sulindac-treated mice, the mucosa was only harvested from areas of inflammation in the proximal colon. For control-fed mice the matching normal tissue was harvested.
|
| Growth protocol |
Homozygous Mcc-loxP (Mccf/f) mice were generated and designated B6.Cg-Mcc<tm1Maija>/Ausb. These were crossed with mice carrying the Villin-cre transgene (B6.SJL-Tg(vil-cre)997Gum/J) to produce colon/intestinal cell specific Mcc knockout mice, VILcreMccf/f (MccΔIEC) and the sibling controls Mccf/f.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen RNeasy mini (Qiagen GmbH, Germany) and measured on the 2100 Bioanalyzer (Agilent).
|
| Label |
Biotin
|
| Label protocol |
Total RNA was converted to cDNA. The cDNA was biotin labeled at the Ramaciotti Centre for Genomics at the University of New South Wales (UNSW, Sydney, Australia), following manufacturers instructions.
|
| |
|
| Hybridization protocol |
cDNA probes were then hybridized to the Mouse Transcriptome Arrays 1.0 as per the manufacturer’s instructions (Affymetrix Ca, USA) at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia).
|
| Scan protocol |
Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.
|
| Description |
WT_MCCf_control_325
|
| Data processing |
Data was RMA normalised using the AffymetrixPowerTools apt-probeset-summarize software (version 1.16.1) (using the -a rma option)
|
| |
|
| Submission date |
Jul 14, 2016 |
| Last update date |
May 01, 2019 |
| Contact name |
Daniel Roden |
| E-mail(s) |
[email protected]
|
| Organization name |
Garvan Institute
|
| Street address |
384 Victoria Street
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20258 |
| Series (1) |
| GSE84391 |
Mouse model of MCC deficiency reveals novel pathways altered by colon barrier destruction in colitis-associated cancer |
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